1nkz

Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Light-harvesting protein B-800/850, alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Light-harvesting protein B-800/850, beta chain × 9 （P26790） Rhodopin b-D-glucoside × 18 octyl beta-D-glucopyranoside × 18 BACTERIOCHLOROPHYLL A × 27 BENZAMIDINE × 9 water × 18	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 36	Light-harvesting protein B-800/850, beta chain × 18 （P26790） Rhodopin b-D-glucoside × 36 octyl beta-D-glucopyranoside × 36 BACTERIOCHLOROPHYLL A × 54 BENZAMIDINE × 18 water × 36	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LHA4_RHOAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 1–53 Author chain C； PDBConstruct 1–53； UniProt 1–53 Author chain E； PDBConstruct 1–53； UniProt 1–53

Light-harvesting protein B-800/850, beta chain

OrganismNot specified

UniProt P26790

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 18	Light-harvesting protein B-800/850, alpha chain × 9 （P26789） Rhodopin b-D-glucoside × 18 octyl beta-D-glucopyranoside × 18 BACTERIOCHLOROPHYLL A × 27 BENZAMIDINE × 9 water × 18	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 36	Light-harvesting protein B-800/850, alpha chain × 18 （P26789） Rhodopin b-D-glucoside × 36 octyl beta-D-glucopyranoside × 36 BACTERIOCHLOROPHYLL A × 54 BENZAMIDINE × 18 water × 36	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LHB5_RHOAC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–41； UniProt 1–41 Author chain D； PDBConstruct 1–41； UniProt 1–41 Author chain F； PDBConstruct 1–41； UniProt 1–41

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1nkz
Deposition date deposition_date	2003-01-06
Structure title title	Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution
Keywords keywords	LIGHT HARVESTING COMPLEX II, TRANS-MEMBRANE HELICES, RHODOPIN GLUCOSIDE, BACTERIOCHLOROPHYLL A, PHOTOSYNTHESIS, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1nkz__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1nkz__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nkz__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	41.88 Å
Rg (electron density)	40.59 Å
Total Rg	41.63 Å
Atom count	19386
Residues	1674
Excluded volume	371850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nkz__assembly_1__model_1`	octadecameric （18）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nkz__assembly_2__model_1`	36-meric （36）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Light-harvesting protein B-800/850, alpha chain
Molecular weight formula_weight	5702.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	3461

MNQGKIWTVVNPAIGIPALLGSVTVIAILVHLAILSHTTWFPAYWQGGVKKAA

Entity 2 Entity 2 polymer

Description description	Light-harvesting protein B-800/850, beta chain
Molecular weight formula_weight	4559.2 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

ATLTAEQSEELHKYVIDGTRVFLGLALVAHFLAFSATPWLH

Entity 3 Entity 3 non-polymer

Description description	Rhodopin b-D-glucoside
Molecular weight formula_weight	715.0 kDa
Source method src_method	man
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	man
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	BACTERIOCHLOROPHYLL A
Molecular weight formula_weight	911.5 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 6 Entity 6 non-polymer

Description description	BENZAMIDINE
Molecular weight formula_weight	120.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	230

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1nkza_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.1 — Light-harvesting complex subunits

Domain ID domain_id	d1nkzb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.1 — Light-harvesting complex subunits

Domain ID domain_id	d1nkzc_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.1 — Light-harvesting complex subunits

Domain ID domain_id	d1nkzd_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.1 — Light-harvesting complex subunits

Domain ID domain_id	d1nkze_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.1 — Light-harvesting complex subunits

Domain ID domain_id	d1nkzf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.3 — Light-harvesting complex subunits
Superfamily Superfamily superfamily	f.3.1 — Light-harvesting complex subunits
Family Family family	f.3.1.1 — Light-harvesting complex subunits

CATH v4.4 (6 domains)

Domain ID domain_id	1nkzA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	1nkzB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	1nkzC00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	1nkzD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

Domain ID domain_id	1nkzE00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	220 — Light-harvesting Protein
Homologous superfamily homologous superfamily	20 — Light-harvesting complex

Domain ID domain_id	1nkzF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	250 —

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Unit-cell length a length_a	117.052 Å
Unit-cell length b length_b	117.052 Å
Unit-cell length c length_c	298.438 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	54

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1704
R_work r_work	0.1694
R_free r_free	0.1901

Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

Light-harvesting protein B-800/850, alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Light-harvesting protein B-800/850, beta chain

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1nkz__assembly_2__model_1

1nkz__assembly_2__model_1 | I(q)

1nkz__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (4)

Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution

1. Protein Identity and Related Structures Protein Identity & Related Structures

Light-harvesting protein B-800/850, alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Light-harvesting protein B-800/850, beta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1nkz__assembly_2__model_1

1nkz__assembly_2__model_1 | I(q)

1nkz__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (4)